"I believe the vessel will reach our shores this evening," Maltese Prime Minister Joseph Muscat said, adding that seven other EU nations -- Italy, Luxembourg, the Netherlands, Portugal, Ireland, Belgium and France -- had also agreed to take some of the migrants.
However, Muscat warned that the situation was "unique" and could not be considered a blueprint for handling future rescues.
Belgium and Luxembourg said they would each take 15 migrants. The Netherlands will take 20.
Theo Francken, Belgian minster for asylum and migration, tweeted that Belgium would help Malta but that it must be one-off operation.
He said his country would only welcome migrants from countries whose asylum requests were often accepted and urged "legal proceedings" against Mission Lifeline.
Muscat said after the migrants disembarked the rescue ship would be impounded pending an investigation.
Mission Lifeline said earlier many passengers were suffering from seasickness and three were in the ship's hospital facility. One passenger has been evacuated, leaving 233 currently on board.
The eight EU nations agreed to take in a share of those on board after days of bickering over the migrants' fate.
However, Italian press reports said Germany had not agreed to participate in the deal, a stance which the NGO's co-founder Axel Steier blamed on the country's hardline Interior Minister Horst Seehofer.
Seehofer has taken a strong stance on immigration and given German Chancellor Angela Merkel an ultimatum to curb arrivals to Germany.
Playing into smugglers' hands
Mission Lifeline has hit back at criticism levelled at it by EU leaders.
On Tuesday, French President Emmanuel Macron said the charity had contravened "all the rules" by rescuing the migrants when the Libya coastguard was already intervening.
Macron accused Mission Lifeline of "playing into the hands of smugglers".
But the charity denied breaking the law in a statement on Wednesday.
"There have been a number of false accusations that Lifeline ignores orders by different MRCCs (maritime rescue coordination centres)," said Steier.
Lifeline argued the migrants would not be safe in Libya, where they have faced abuse and rape in holding centres, and that returning them there would breach international refugee law.
"The only order the ship denied was to hand over people to the so-called Libyan coastguard, as this would have been not in line with the Geneva Refugee Convention and therefore criminal."
The vessel's fate has hung in the balance since last week as bloc members remained at loggerheads over how to handle the influx of people trying to reach the continent.
Malta and Italy initially refused to take in the migrants, but on Tuesday Valletta agreed to let the ship dock when other EU states confirmed they would help.
Italy's far-right Interior Minister Matteo Salvini had hailed the news that a second migrant ship he had turned away would be taken in elsewhere.
Earlier this month, Rome rejected the Aquarius ship carrying 630 migrants, forcing it to eventually dock in Spain.
"For women and children really fleeing the war the doors are open, for everyone else they are not!" Salvini tweeted.
The decision by Italy's new hardline government to turn away rescue vessels has plunged Europe into a political crisis over how to collectively handle the huge numbers of people migrating from Africa, the Middle East and Asia.
Italy and Malta say they are unfairly bearing the brunt of the new arrivals, while other European countries are urging more forceful policies to block their entry.
jpegMpeg4-1280x720Sixteen EU leaders held emergency talks in Brussels on Sunday in a bid to break the longstanding deadlock over who should take in the migrants.
A full EU summit is scheduled for Thursday and Friday.